Ontology meeting 2015-02-12

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Attendees:Harold, Paola, David H, David OS, Heiko, Tanya, Harold

Minutes:David

Enzyme Binding

We have decided that we will include families. How we define families will need to be addresses. Is it only if there is more than one similar gene in the same organism? The bottom line here is that a gene protein is not binding the activity, it is binding the molecule.

Disjoints in ChEBI

David OS to report back on today's meeting with Janna.

Punt until Chris is around. We will set up a Jenkins job to send to them about disjoints. We can make a branch file with high-level disjoints that we can edit ourselves and test. We can then feed this to them. Perhaps we can set up a Jenkins job to run Chebi and find violations that will become obvious to address.

Regulation Chains (punt to next week when Judy is attending)

David H will go over Nikolai's results chaining regulates relations and introducing direct and indirect regulation.

- Related (may want to punt to next week):

  * Inference resulting from implementing regulation chain reasoning
  * results_in relations - how does this fit?  Currently no axiomatisation linking this to regulates.  Shouldn't there be?

Release process: relaxing equivalent class (intersections) to subclassof

During our current release process, we do not generate subClassof axioms (relationships) from EquivalentClass axioms (intersections). This means that they need to be added by hand to show up. (Failure to do this has lead to a few SF requests that really should be uncessesary e.g. https://sourceforge.net/p/geneontology/ontology-requests/11465/).

I assume that this is not done because we don't want all the whole zoo of relations we use in equivalent class axioms to show up in the regular GO release files. But these two issues really should be decoupled. They already are for other OBO ontologies using OORT & owltools for their release process. (see FBbt, CL...).

Please could fixing this be made a high priority?

The reasons might be that we have a step that removes relations so that they do not end up in the processed files. Can we have a release that only filters out the relations that we don't want, but keeps the ones that are allowed? We will ask Chris about this.

Defining has_regulation_target and related relations

(see email subject: [go-ontology] Proposal for has regulation target)

Proposal

  • regulation MF has_regulation_target(UniProtKB:protein Y) protein X regulates the kinase activity of protein Y
  regulates o mediated_by -> has_regulation_target
  • regulation BP has_regulation_target(UniProtKB:protein Y) protein X regulates the localization of protein Y to the membrane
  • >
  • regulation BP regulates_transport_of(UniProtKB:protein Y) protein X regulates the localization of protein Y to the membrane
  regulates o 'transports or maintains localization of' ->  regulates_transport_of: 
  • Review other uses for has_regulation_target and define relevant regulates over relation

Jira tickets

Need to review the situation with Chris. (Paola has a list of tickets that need special attention. For my own reference, they're in an email thread "GO tickets in the EBI Jira instance".)

Can we clean these up? We should all look at our items.

Much discussion about synonyms. AI: David will ping Judy about synonyms.

Follow-up: Sources of db_xrefs

Action items from last meeting? http://wiki.geneontology.org/index.php/Ontology_meeting_2015-02-05#Sources_of_db_xrefs

results_in_fusion_of

Should this be a subproperty of results_in_organisation_of?

https://sourceforge.net/p/geneontology/ontology-requests/11406/

More broadly - can we plan some time to review the position of results_in_fu relations in the hierarchy? I suspect more can be pushed under 'has participant' &/or results in organisation of.